Ionisation potential and electron affinity of free 5′,8-cyclopurine-2′-deoxynucleosides. DFT study in gaseous and aqueous phase

Karwowski, Bolesław T.

doi:10.2478/s11532-009-0105-0

Cited by 8 publications

(7 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For all the optimized geometries, a charge and spin analysis was achieved using Hirshfeld methodology at the M06-2X/6-31++G** level of theory [ 18 ]. The electronic properties of molecules were calculated as described previously: for further details, please see references [ 18 , 19 ]. The characterization of the transition dipole moment of excited states and the single point calculation at the M06-2X/6-31++G** level of theory were performed using time-dependent DFT (TD-DFT) methodology [ 20 ].…”

Section: Methodsmentioning

confidence: 99%

How Clustered DNA Damage Can Change the Electronic Properties of ds-DNA—Differences between GAG, GAOXOG, and OXOGAOXOG

Karwowski

2023

Biomolecules

View full text Add to dashboard Cite

Every 24 h, roughly 3 × 1017 incidences of DNA damage are generated in the human body as a result of intra- or extra-cellular factors. The structure of the formed lesions is identical to that formed during radio- or chemotherapy. Increases in the clustered DNA damage (CDL) level during anticancer treatment have been observed compared to those found in untreated normal tissues. 7,8-dihydro-8-oxo-2′-deoxyguanosine (OXOG) has been recognized as the most common lesion. In these studies, the influence of OXOG, as an isolated (oligo-OG) or clustered DNA lesion (oligo-OGOG), on charge transfer has been analyzed in comparison to native oligo-G. DNA lesion repair depends on the damage recognition step, probably via charge transfer. Here the electronic properties of short ds-oligonucleotides were calculated and analyzed at the M062x/6-31++G** level of theory in a non-equilibrated and equilibrated solvent state. The rate constant of hole and electron transfer according to Marcus’ theory was also discussed. These studies elucidated that OXOG constitutes the sink for migrated radical cations. However, in the case of oligo-OGOG containing a 5′-OXOGAXOXG-3′ sequence, the 3′-End OXOG becomes predisposed to electron-hole accumulation contrary to the undamaged GAG fragment. Moreover, it was found that the 5′-End OXOG present in an OXOGAOXOG fragment adopts a higher adiabatic ionization potential than the 2′-deoxyguanosine of an undamaged analog if both ds-oligos are present in a cationic form. Because increases in CDL formation have been observed during radio- or chemotherapy, understanding their role in the above processes can be crucial for the efficiency and safety of medical cancer treatment.

show abstract

Section: Methodsmentioning

confidence: 99%

How Clustered DNA Damage Can Change the Electronic Properties of ds-DNA—Differences between GAG, GAOXOG, and OXOGAOXOG

Karwowski

2023

Biomolecules

View full text Add to dashboard Cite

show abstract

“…For all the optimized geometries, charge, and spin analyses were achieved using the Hirshfeld methodology at the M06-2X/6-31++G** level of theory [ 31 ]. The electronic properties of molecules were calculated as described previously [ 35 , 54 ]. The transition dipole moment of excited states and the single point calculation at the M06-2X/6-31++G** level of theory were performed using time-dependent DFT (TD-DFT) methodology [ 55 ].…”

Section: Methodsmentioning

confidence: 99%

FapydG in the Shadow of OXOdG—A Theoretical Study of Clustered DNA Lesions

Karwowski

2023

IJMS

View full text Add to dashboard Cite

Genetic information, irrespective of cell type (normal or cancerous), is exposed to a range of harmful factors, which can lead to more than 80 different types of DNA damage. Of these, oxoG and FapyG have been identified as the most abundant in normoxic and hypoxic conditions, respectively. This article considers d[AFapyGAOXOGA]*[TCTCT] (oligo-FapyG) with clustered DNA lesions (CDLs) containing both the above types of damage at the M06-2x/6-31++G** level of theory in the condensed phase. Furthermore, the electronic properties of oligo-FapyG were analysed in both equilibrated and non-equilibrated solvation–solute interaction modes. The vertical/adiabatic ionization potential (VIP, AIP) and electron affinity (VEA, AEA) of the investigated ds-oligo were found as follows in [eV]: 5.87/5.39 and −1.41/−2.09, respectively. The optimization of the four ds-DNA spatial geometries revealed that the transFapydG was energetically privileged. Additionally, CDLs were found to have little influence on the ds-oligo structure. Furthermore, for the FapyGC base-pair isolated from the discussed ds-oligo, the ionization potential and electron affinity values were higher than those assigned to OXOGC. Finally, a comparison of the influence of FapyGC and OXOGC on charge transfer revealed that, in contrast to the OXOGC base-pair, which, as expected, acted as a radical cation/anion sink in the oligo-FapyG structure, FapyGC did not significantly affect charge transfer (electron–hole and excess–electron). The results presented below indicate that 7,8-dihydro-8-oxo-2′-deoxyguanosine plays a significant role in charge transfer through ds-DNA containing CDL and indirectly has an influence on the DNA lesion recognition and repair process. In contrast, the electronic properties obtained for 2,6-diamino-4-hydroxy-5-foramido-2′deoxypyrimidine were found to be too weak to compete with OXOG to influence charge transfer through the discussed ds-DNA containing CDL. Because increases in multi-damage site formation are observed during radio- or chemotherapy, understanding their role in the above processes can be crucial for the efficiency and safety of medical cancer treatment.

show abstract

“…Here it should be noted that the recent development of computational capabilities and methodologies have triggered intense activity in the theoretical community to understand the processes in DNA damage, light harvesting, etc. − Dominant pathways for the photoprotection and photodamage of isolated DNA bases have been studied extensively. There has been similar success from the theoretical perspective in various other photoprocesses of small molecules. − …”

Section: Introductionmentioning

confidence: 92%

Hybrid Equation-of-Motion Coupled-Cluster/Effective Fragment Potential Method: A Route toward Understanding Photoprocesses in the Condensed Phase

Ghosh

2016

J. Phys. Chem. A

View full text Add to dashboard Cite

The prediction of accurate solvatochromic shifts to the electronic excited states of chromophores is a challenge, especially in the complex biological phase, due to the importance of long-range electrostatic interactions. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are generally employed for the calculation of quantum mechanical properties in complex systems. To be predictive, there is need for an accurate quantum mechanical method that can depict the charge transfer states correctly and incorporate higher than single excited determinants in its linear response ansatz. On the contrary, for the correct depiction of the environment interactions (MM region), one needs to account for polarizability in a balanced manner. These two challenges are successfully addressed by the recently developed hybrid quantum mechanical/effective fragment potential (QM/EFP) methods, with equation-of-motion coupled-cluster (EOM-CC) as the QM method of choice. The result is an efficient method to estimate excitation energy, ionization energy, electron affinity, and redox potential in the condensed phase. It has further been extended to biological systems.

show abstract

Ionisation potential and electron affinity of free 5′,8-cyclopurine-2′-deoxynucleosides. DFT study in gaseous and aqueous phase

Cited by 8 publications

References 24 publications

How Clustered DNA Damage Can Change the Electronic Properties of ds-DNA—Differences between GAG, GAOXOG, and OXOGAOXOG

How Clustered DNA Damage Can Change the Electronic Properties of ds-DNA—Differences between GAG, GAOXOG, and OXOGAOXOG

FapydG in the Shadow of OXOdG—A Theoretical Study of Clustered DNA Lesions

Hybrid Equation-of-Motion Coupled-Cluster/Effective Fragment Potential Method: A Route toward Understanding Photoprocesses in the Condensed Phase

Contact Info

Product

Resources

About